Bob,
On 9/15/2010 11:47 AM, Robert Hanson wrote:
Charges at atoms have to be summed using q/r for each point on the
isosurface. So the values at the surface are different from the values
at the atoms (smaller values). For example:
OK, I get it. The first data range in the message is the data range for
the computed surface charge points. If I use "color range all," then the
following message type is returned:
data range 0.28645405 to 0.5315478 with color scheme spanning 0.28645405
to 0.5315478
The expression "color scheme spanning" takes on the value of the
calculated surface data range. If however, in the Jmol script, I set a
color range based on the actual atomic charges, then this "color scheme
spanning" reports the value of my Jmol script charges. Is this just a
message reporting peculiarity? If I want to set an actual range in Jmol
script, are the actual atomic charges the values that I should use as my
guide?
Right now, Jmol 11 ignores any charges on atoms more than 8 angstroms
away from a given point, which doesn't mean much for small models.
More significantly, though, Jmol right now creates a "field" of
potential around the model and then uses that to map the surface. This
isn't really necessary -- you can just pick a surface point and sum
all the q/d from all the atoms. I've just rewritten the code for 12.0
and 12.1 to do that and will get that in the next release.
Related to this, I'm not sure that I understand varying Jmol surface
dimensions. Am I correct that these are the options for creating a
surface to map?
1) Solvent
2) Molecular
3) van der Waals at settable % values
The reason that I ask this is that Spartan creates something called a
bond surface map, and I'm trying to translate that into Jmol thinking.
Otis
Bob
On Mon, Sep 13, 2010 at 9:10 PM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
The data range 0.41223556 to 0.6573585 seems to vary with the partial
charges, but seems unrelated to the actual partial charges. The result
below is for "range all" on the allyl cation and benzyl cation,
respectively. In the snippet above, I was just trying out values other
than "range all."
full data range 0.41223556 to 0.6573585 with color scheme spanning
0.41223556 to 0.6573585
data range 0.28645405 to 0.5315478 with color scheme spanning
0.28645405
to 0.5315478
All of this is part of my attempt to make Spartan charge numbers work
well with Accelrys charge numbers. Can you give me any information on
the origin of these numbers - calculated from my charges???
Otis
PS
Thanks for the feedback on the array question.
--
Otis Rothenberger
chemagic.com <http://chemagic.com>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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